The use of probiotics is considered an attractive biocontrol method. It is effective in growth promotion in aquaculture. However, the mode of action of probiotics in fish in terms of growth promotion remains unclear. The objective of the present study was to investigate growth promotion effect of dietary administration of host-derived probiotics, Lactococcus lactis WFLU12, on olive flounder compared to control group fed with basal diet by analyzing their intestinal and serum metabolome using capillary electrophoresis mass spectrometry with time-of flight (CE-TOFMS). Results of CE-TOFMS revealed that 53 out of 200 metabolites from intestinal luminal metabolome and 5 out of 171 metabolites from serum metabolome, respectively, were present in significantly higher concentrations in the probiotic-fed group than those in the control group. Concentrations of metabolites such as citrulline, tricarboxylic acid cycle (TCA) intermediates, short chain fatty acids, vitamins, and taurine were significantly higher in the probiotic-fed group than those in the control group. The probiotic strain WFLU12 also possesses genes encoding enzymes to help produce these metabolites. Therefore, it is highly likely that these increased metabolites linked to growth promotion in olive flounder are due to supplementation of the probiotic strain. To the best of our knowledge, this is the first study to show that dietary probiotics can greatly influence metabolome in fish. Findings of the present study may reveal important implications for maximizing the efficiency of using dietary additives to optimize fish health and growth.